Description
The DeepChek® Assay Whole Genome SARS-CoV-2 Genotyping is a RT-PCR Assay (nucleic acid technique (NAT)) followed by Next Generation Sequencing (NGS) intended to aid clinical applications and for use on previously diagnosed COVID-19 patients.
Application (RUO) — REF 159D48
For Research Use Only (RUO). Not for use in diagnostic procedures. No claim or representation is intended to provide information for the diagnosis, prevention, or treatment of disease.
The DeepChek Assay Whole Genome SARS-CoV-2 Genotyping (RUO) is a reverse transcriptase (RT) polymerase chain reaction (PCR) test (nucleic acid technique (NAT)) intended to screen the emergence of SARS-CoV-2 genome mutations using extracted RNA from patients already diagnosed PCR positive to SARS-CoV-2.
The test is amplifying the whole genome of the SARS-CoV-2, including regions which harbor mutations described as sufficient, when present, to characterize some variants.
Results are used to build basic research knowledge and evidence on the emergence of circulating SARS-CoV-2 variants.
Results are used to better understand SARS-CoV-2 transmission and to monitor for the emergence of new variants, even in minor viral populations, through ongoing epidemiological surveillance and strategic testing; conducting outbreak investigation and contact tracing; and where appropriate, adjusting public health and social measures to reduce transmission of SARS-CoV-2.
The DeepChek Assay Whole Genome SARS-CoV-2 Genotyping (RUO) is intended for use by trained clinical laboratory personnel specifically instructed and trained in the techniques of RT-PCR and next generation sequencing (NGS) workflow.
Methodology
Reverse Transcriptase Polymerase Chain Reaction (RT-PCR) and Next Generation Sequencing.
The Assay targets and amplify the whole genome (>99%) of SARS-CoV-2 virus, including regions that harbor mutations of interest described as sufficient in databases like Pangolin and Nextclade, including variants of concern (VOC).
Post PCR – Complementary information
Next Generation Sequencing
The main volume of the product output is then used for next generation sequencing (NGS). The NGS workflow can be
different as the NGS technics and NGS analyzers vary. NGS sequencing instruments are general laboratory use devices.
Sequencing and library preparations reagents are general laboratory use products.
While the verification studies, we used the Illumina iSeq 100 Sequencing System (#20021532) and the following combination
of reagents: ABL DeepChek® NGS Library preparation (catalog #116BX, 24 or 48 or 96 tests), ABL DeepChek® Assay Adapters (catalog #124BX, 1-24, 1-48 or 1-96) and Illumina iSeq 100 Reagent (catalog # 20021533, 300 cycles).
Downstream NGS Analysis Software
The next generation sequencing raw data are uploaded in a specific downstream software tailored for SARS-CoV-2 analysis which is a standalone medical device (i.e. DeepChek CoV2 software (RUO) license and module (REF S-12-023 (CVL) and S-12-023 (CVM)). The software itself could be CE-IVD marked and shall refer to an updated expert list of mutations and variants per virus lineages with latest knowledge and analyses.
More information on the DeepCheck® SARS CoV-2 Whole Genome – Click here
Characteristics and performances
Features
RT-PCR Assay followed by NGS (Next Generation Sequencing)
>99% genome covered by Multiplex targeting SARS CoV-2 whole genome
RNA extraction and purification of clinical specimen
MagNa Pure 24 instrument (Roche;
Catalog #07290519001B) with the MagNA Pure 24 Total NA Isolation Kit (Roche, Catalog #07658036001)
Note: Any laboratory validated instrument for RNA extraction and purification using magnetic-bead technology shall work
with the test (i.e. bioMérieux EMAG®, Perkin Elmer ChemagicTM 360, ThermoFisher Scientific MagMAX Viral/Pathogen
Nucleic Acid Isolation Kit, Qiagen QIAamp Viral RNA Mini Kit, Biopur® Mini Spin Plus Kit and Magtivio MagSi-NA Pathogens).
PCR
ThermoFisher Scientific ProFlex™ PCR System (model 3 x 32-well (Catalog #4484073) or 96-well (Catalog
#4484075) and associated specific material.
Note: Any laboratory validated thermal cycler with enough ramp rate of ≥ 1°C/s shall be sufficient.
Validated with NGS platforms
- iSeq-100
- Miseq
Note: Any laboratory validated instrument for NGS shall work with the test
Format / Models
- 48 tests/kit (159A48)
Content
- CoV Reaction Solution (Master Mix 2X, RT Mix)
- Whole Genome Primers
- Positive Control
- Negative Control
- Molecular Grade Water
Hands-on-time
2h30
Estimated turnaround time
[48 - 72 h]
Limit of Detection (LoD)
1250 cp/mL
The concentration level for the DeepChek Assay Whole Genome SARS-CoV-2 Genotyping V1 with observed rates greater
than or equal to 95% was 0.000115 TCID50/mL for SARS-CoV-2 with the ProFlex™ 3 x 32-well PCR System (Catalog
#4484073).
Analytical specificity
Among the tested samples with specific clades (UK or SA): 100% were adequately amplified, sequenced and characterized, either as B.1.1.7 or B.1.351, by the DeepChek CoV2 software following the DeepChek Assay Whole Genome SARS-CoV-2 Genotyping V1.
Inclusivity (analytical reactivity)
The DeepChek Assay Whole Genome SARS-CoV-2 Genotyping V1 has excellent coverage of all reported circulating SARS-CoV-2 strains in the Inclusivity dataset (121 358 unique sequences after removal of low identity and low coverage alignments)
Cross-reactivity (In Silico )
All pathogens were determined to have no cross-reactivity with the primers pairs used for the the DeepChek Assay Whole Genome SARS-CoV-2 Genotyping V1
Cross-reactivity (Wet testing)
For cross-reactivity wet testing, the DeepChek Assay Whole Genome SARS-CoV-2 Genotyping V1 did not react for most of the tested microorganisms that are commonly found in upper respiratory specimens and tested at the indicated concentration
Clinical sensitivity
The positive (PPA) and negative (NPA) percent agreements between the DeepChek Assay Whole Genome SARS-CoV-2
Genotyping V1 and the CE-IVD comparator assay are:
PPA = 30/30 = 100% (95% C.I. = 88.65% - 100%)
NPA = 30/30 =
100% (95% C.I. = 88.65% - 100%)
The agreement between the two tests (93.5%) was perfect (Cohen’s kappa = 0.87) for variants detection
Clinical reproducibility
100% results accuracy both for SARS-CoV-2 clade identification and defining mutations used for clade identification (Nexstrain SARS-CoV-2)
External clinical validation
Among the 255 successful samples, the SARS-CoV-2 clades identified as variants of concern (VOC) (n=102, 40.0%) were identified with 29.4% (20H/501Y.V2)(SA), 5.9% (20J/501Y.V3)(BR) and 4.7% (20I/501Y.V1) (UK1). Among the other SARSCoV-2 clades identified, the DeepChek Assay Whole Genome SARS-CoV-2 Genotyping V1 detected one of the first cases in France for the Indian double mutant (20A/484Q (B.1.617)). A subset of 10 samples (extracted RNA) were also sent for results validation by the French SARS-CoV-2 CNR (Centre National de Référence des virus respiratoires): 100% results accuracy was reached with the CNR whole genome sequencing workflow and the DeepChek Assay Whole Genome SARSCoV-2 Genotyping V1
Workflow
Ordering information
Product
Reference
GTIN
DeepChek Assay Whole Genome SARS-CoV-2 Genotyping V1 (48 tests) (CE-IVD)
159A48
05407007960217
Downloads
DoC
-
EC Declaration of Conformity
Request of Documentation (IFU, MSDS, CoA, ...)
Related products
DEEPCHEK® ASSAYS
Sequencing-based genotyping assays for microbiolog…
The DeepChek® Assay product line combines target-specific PCR reagents with in vitro diagnostic software both compatible with either Sanger or Next Ge…
DEEPCHEK® SOFTWARE
Downstream Sequencing Data Analysis and Interpreta…
DeepChek® is a downstream analysis software developed by ABL, able to handle sequencing data and intended to be used for performing genomic data analy…